> Regardless of what HUGO is, a comparison of Venter and Watson should
> highlight some locations that are different, should it not?

Yes, it should. This is the leading edge of the new era of
whole-chromosome genetic genealogy. These two men may share
a common ancestor a hundred or so generations ago, and they
therefore probably differ at a hundred or so loci on the Y
chromosome. Indeed, if we knew the average single-nucleotide
mutation rate appropriate to the places their ancestors lived,
we could determine with fair accuracy when their MRCA lived.

Comparison to HUGO could presumably determine which of the two
men has the ancestral base, and which has the mutation, at each
discrepant locus.

Comparison to another male in the same clade would not only reveal
some additional SNPs "private" to the other man's line, but also
determine the relative TMRCA of each pair among the three. Some
of the SNPs in one of the men would be revealed as "upstream"
relative to all the rest.

This is the start of a whole-chromosome-based phylogenetic tree that
would in principle resolve *every* male's position with regard to
everyone else's and, in effect, identify a "clade" for everyone
tested, as well as for the known common ancestors established by
conventional genealogy.

In the new era, the STR data and the one-at-a-time SNP system we now
see will all be left in the dust. Each male can be identified
uniquely (or nearly so) by a string of a few thousand SNPs, and the
cumbersome extendable clade system will be replaced by a permanent,
but terribly verbose, classification scheme that only a computer could
love. In principle, it really will be possible to sample a man's DNA
and then crank out a "complete" male-line family tree (of course
conflating all segments of the tree consisting of men who have only
one son with tested descendants).